Imaging data processing apparatus and imaging data processing program to perform image alignment by deforming images such that imaged observation target sites coincide

In a data processing unit, alignment is performed by appropriately deforming one image among MS imaging images acquired from different samples so that positions and sizes on the MS imaging image are matched (S1 to S5). When the aligned image is displayed on a screen of a display unit and a user sets a region of interest on the image serving as a reference (S6), a micro region including a center point within a range of the set region of interest is extracted in each of an image serving as the reference and an image not serving as the reference (S7). In the image subjected to image deformation, although the shape of each micro region is distorted and micro regions are not arranged in an orderly grid manner, by assuming that the micro regions in which the center point is included within the range of the region of interest is included in the range of the region of interest, it is possible to perform a comparative analysis based on the data value within an appropriate micro region corresponding to the region of interest regardless of the image deformation.